Saturday, April 2, 2011

How to bead weave DNA double helix earrings

I got such a great response to my beaded DNA earrings that I thought I'd release the pattern as a free video, made with Doceri software.

Be forewarned... this weave is not as easy as it looks. It requires careful attention to tension or the beadwork won't end up stiff and hold its spiral. That said, you should still try it out, and let me know what you think. If you do, I hope you'll show me what you make!

If you just want to have a pair of DNA earrings, without having to go to all of the trouble to make them yourself, I usually have a few pairs for sale in the earrings section of my Etsy shop.
The video shows how to weave a sequence of 5 base pairs recognized from the species Thermus aquaticus. According to Cindy Holsclaw (beadorigami), T. aquaticus is, "the source of Taq DNA Polymerase, which greatly streamlined the technique of the polymerase chain reaction (PCR), turning it into the indispensable component of biotechnology used today."

COLORING THE BASE PAIRSBelow is a different photo of one of the pairs of earrings I show in the video. Notice I matched the gray matte beads with copper matte beads, and the shiny gold metallic ones with shiny red metallic.

The sequence of colors on this pair runs through all four possible pairings: 1~3, 3~1, 2~4 and 4~2. I repeated the four pairings 3 times plus one more base pair, for a total of 3*4 + 1 = 13 base pairs. While the beader in me used four colors of beads, the mathematician in me used numbers to represent this sequence so I had a pattern to follow while I beaded. 1234 1234 1234 13412 3412 3412 3where the 1 is always paired with 3, and 2 is paired with 4.However, in terms of DNA, we use the following pairs of molecules: A~T, T~A, C~G, and G~C. Thus, a molecular biologist might write the sequence ACTG ACTG ATCG A TGAC TGAC TGAC T or possibly, CTGA CTGA TCGA CGACT GACT GACT Gbut in neither case, do I know of any real genetic code that displays this sequence, but with all of the DNA in the human genome, it must be in there somewhere.

After I made the pair above, Cindy Holsclaw pointed me towards some cool links on DNA sequences recognized by restriction enzymes. The sequences in the tables are short (but still in a variety of lengths), and they exhibit nice symmetry, which I think is more interesting than the DNA sequence I used above. I suggest you check out this list about enzymes; do it for the molecular biologist in you. I learned a lot by clicking through the table, and it lead me to make this pair of earrings.

In this pair, the coloring of the base pairs comes from the enzyme PpiI which is found in the microorganism Pseudomonas putida. Pseudomonas putida is a safe strain of soil bacterium, and is the first patented organism in the world. Because it is a living organism the patent was disputed and brought before the United States Supreme Court in the historic court case Diamond v. Chakrabarty which the inventor, Ananda M. Chakrabarty, won. It demonstrates the ability to biodegrade organic solvents such as oil. The specific base pair sequence shown in each earring is
GAACN5CTC
CTTGN5GAG
The N5 means there are 5 Ns there, like NNNNN. In chemistry, these could be any of G, A, C, or T. Rather than choose a random sequence of colors, I used matte black beads for all the Ns. I like the way the coloring worked in this pair. I was surprised to find that the symmetry and structure of the coloring actually makes me think that it's supposed to mean something. I am very pleased with this revelation.

TWIST THE NIGHT AWAY!
One final note on chirality, or the handedness with which I twisted the strands. In terms of beads, the beadwork is flexible, and you can untwist and retwist a helix to make it either handedness, what a spinner would call an S-twist (left) or a Z-twist (right). In terms of chemistry, most of these strips of DNA usually only appear in one chirality, and so it's the artist in me that takes liberties and twists them makes them a mirrored, matching pair of earrings.

SPLIT DNA NECKLACE Here's an idea for a necklace I want to try... Make a Y-shaped necklace, where the two sides of the DNA split and become two identical double helices, just like real DNA splits to reproduce itself.

ERRATA I received a couple very helpful and informative emails from Professor of Biochemistry, Becca Dickstein, and she set me straight about the sequences I used in my earrings and the video. Professor Dickstein writes, "... the sequences... recognized by the restriction enzymes and are not part of the enzymes. The enzymes are sometimes thought of as molecular scissors and they recognize a particular sequence in the DNA. Most of them also cut at that sequence, but some of them recognize at one site and then cut several to many nucleotides away. (Nucleotides are the bases of DNA: A, G, C, and T, connected to deoxyribose sugars and phosphates.) The table that Cindy Holsclaw sent you to has the recognition sequences, and the cut sites as well, and you can see that in some cases they are different. The table also has isoschizomers listed. These are enzymes from different organisms that recognize the same set of bases." So, one thing I said in the video about the sequence was technically incorrect since the DNA sequences are not actually found in the enzymes. I apologize for this error. Live and learn.

Professor Dickstein further suggests that "if you want to know more about restriction enzymes, a company that sells them is New England Biolabs and you can find a lot of information about them at www.neb.com."

18 comments:

Really nice! I too have had a DNA structure on my to do list for a while. My idea uses RAW so it's bigger, more suitable for a necklace than earrings, but I really like yours. I loved watching the video, too, because I've always thought about teaching how to create structures, but never done it. The to do list just gets longer. Anyway, great stuff.

Thank you Emilie. Beading DNA was remarkable elusive for me for several years, but I finally got it. It only took me 8 tries to get this pattern to work as I like it. Have you posted any photos of your version? I'd love to see it!

Thanks for another great video tutorial, Gwen. I didn't think I'd try the DNA structure at first, but your instructions are so well done they are irresistible. I think I'll have to put my thinking cap on and see what I can come up with to use this pattern. Thank you so much for sharing it!

With regard to the sequence in your first pair of earrings, a quick search reveals that the sequence ACTGACTGATCGA is present in the human genome a couple dozen times, which isn't surprising, considering that the human genome consists of over 3 billion (yep, billion!) base pairs. It doesn't appear to be present in the 1.5% of the human genome that codes for proteins though. But, a broader search that includes other organisms results in several hits in such "coding sequences." The most interesting hit that I found is in a plant version of a gene that codes for a special kind of DNA replication enzyme used in DNA repair. The molecular mechanism of this repair is Really Cool, but if I attempt to explain it I'd launch into much more biogeekery and I'd be here for days...

Anyway, information for the gene in question can be found here: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=834503

Cindy, you are too awesome for words! I love that I can just make up a sequence, and you find it in the genome. I feel like a monkey typing Shakespeare. Thank you! But I have to say, I really prefer the look of the subtle symmetries found in the sequences recognized by the restriction enzymes. There's something very pleasing about them when rendered as in beads.

Thanks Gwen for this great tutorial and inspiring earrings! Again, well done for the smart design. As a former biologist I had to try it, it was only a matter of time. I like so much the idea of making a DNA related scene, based on this design. This can be such a cool project, adding all the involved enzymes as beaded beads...hmmm...http://judith27k.blogspot.com/2011/06/19611-dna-earrings-by-gwen-fisher.html

Thanks a lot for this video ! I totally fell in love with your DNA earrings, I now have to buy a nice set of 8/0 seed beads and 3mm bugles :) !

I also take the opportunity to say "BRAVO" to you and Florence for your beadinfinitum website. I had never thought of mathematical beading before, I just love your artistical-scientific way of beading. It's open-minding :).

Definitely having me a little nerd-on here. As a former psych major whose daughter has a genetically derived disability, I was looking for a way to make a bracelet to sell to support my life at home with her... You've inspired me to be scientifically accurate and look up my favorite gene to research (GABRB3) in the region where she has an isodicentric chromosome resulting in tetrasomy.... with over 200,000 base pairs in the gene, I can keep making one-of-a-kind bracelets for a very long time to honor her abilities and challenges and raise awareness for her disability (IDIC 15q 11.2-13.1) and the role that GABA transmitters play in autism in recent research. Squeee!!!!

I really love this project! I've been meaning to make something handmade to sell to support my life at home- I stay home with our daughter to have more time to teach her and do therapy, as she has an isodicentric duplication of a portion of her 15th chromosome- IDIC 15q 11.2-13.1 ... I decided to start at the beginning of the sequence of the GABRB3 gene because of the role that one of my professors said GABA transmitters play in autism. This is one of the few maternally/paternally methylated genes in this gene sequence which causes IDIC 15 syndrome, Angelman's and Prader-Willi Syndrome (all of which have autistic features), and it interests me greatly. I appreciate the design so WISH ME LUCK! as I interpret it for my own devices. Please feel free to contact me to object if need be, if you do not like the idea of my selling the design. THANKS for the nerd-on!